Mercurial > repos > iuc > gatk2
annotate realigner_target_creator.xml @ 6:35c00763cb5c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
| author | iuc |
|---|---|
| date | Mon, 04 Jun 2018 05:38:15 -0400 |
| parents | f244b8209eb8 |
| children |
| rev | line source |
|---|---|
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
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4
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changeset
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1 <tool id="gatk2_realigner_target_creator" name="Realigner Target Creator" version="@VERSION@.1"> |
| 0 | 2 <description>for use in local realignment</description> |
| 3 <macros> | |
| 4 <import>gatk2_macros.xml</import> | |
| 5 </macros> | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
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changeset
|
6 <expand macro="requirements" /> |
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
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changeset
|
7 <expand macro="version_command" /> |
| 0 | 8 <command interpreter="python"> |
| 9 gatk2_wrapper.py | |
| 10 --stdout "${output_log}" | |
| 11 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input" | |
| 12 #if str( $reference_source.input_bam.metadata.bam_index ) != "None": | |
| 13 -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index | |
| 14 #end if | |
| 15 -p ' | |
| 16 @JAR_PATH@ | |
| 17 -T "RealignerTargetCreator" | |
| 18 -o "${output_interval}" | |
| 19 | |
| 20 \$GATK2_SITE_OPTIONS | |
| 21 | |
| 22 ## according to http://www.broadinstitute.org/gatk/guide/article?id=1975 | |
| 23 --num_cpu_threads_per_data_thread 1 | |
| 24 | |
| 25 @THREADS@ | |
| 26 | |
| 27 #if $reference_source.reference_source_selector != "history": | |
| 28 -R "${reference_source.ref_file.fields.path}" | |
| 29 #end if | |
| 30 ' | |
| 31 #set $rod_binding_names = dict() | |
| 32 #for $rod_binding in $rod_bind: | |
| 33 #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom': | |
| 34 #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name | |
| 35 #else | |
| 36 #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector | |
| 37 #end if | |
| 38 #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1 | |
| 39 -d "-known:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" | |
| 40 #end for | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
41 |
|
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
42 $allow_n_cigar_reads |
| 0 | 43 #include source=$standard_gatk_options# |
| 44 ##start analysis specific options | |
| 45 #if $analysis_param_type.analysis_param_type_selector == "advanced": | |
| 46 -p ' | |
| 47 --minReadsAtLocus "${analysis_param_type.minReadsAtLocus}" | |
| 48 --windowSize "${analysis_param_type.windowSize}" | |
| 49 --mismatchFraction "${analysis_param_type.mismatchFraction}" | |
| 50 --maxIntervalSize "${analysis_param_type.maxIntervalSize}" | |
| 51 ' | |
| 52 #end if | |
| 53 </command> | |
| 54 <inputs> | |
| 55 <conditional name="reference_source"> | |
| 56 <expand macro="reference_source_selector_param" /> | |
| 57 <when value="cached"> | |
| 58 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &lt;input_file&gt;"> | |
| 59 <validator type="unspecified_build" /> | |
| 60 <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select --> | |
| 61 </param> | |
| 62 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;" > | |
| 63 <options from_data_table="gatk2_picard_indexes"> | |
| 64 <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> | |
| 65 </options> | |
| 66 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 67 </param> | |
| 68 </when> | |
| 69 <when value="history"> | |
| 70 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &lt;input_file&gt;" /> | |
| 71 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;"> | |
| 72 <options> | |
| 73 <filter type="data_meta" key="dbkey" ref="input_bam" /> | |
| 74 </options> | |
| 75 </param> | |
| 76 </when> | |
| 77 </conditional> | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
78 |
| 0 | 79 <repeat name="rod_bind" title="Known Variants" help="Using data sets of known variants (-known,--known &lt;known&gt;)"> |
| 80 <conditional name="rod_bind_type"> | |
| 81 <param name="rod_bind_type_selector" type="select" label="Variant Type"> | |
| 82 <option value="dbsnp" selected="True">dbSNP</option> | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
83 <option value="snps">SNPs</option> |
| 0 | 84 <option value="indels">INDELs</option> |
| 85 <option value="custom">Custom</option> | |
| 86 </param> | |
| 87 <when value="dbsnp"> | |
| 88 <param name="input_rod" type="data" format="vcf" label="Variant file (VCF format)" /> | |
| 89 </when> | |
| 90 <when value="snps"> | |
| 91 <param name="input_rod" type="data" format="vcf" label="Variant file (VCF format)" /> | |
| 92 </when> | |
| 93 <when value="indels"> | |
| 94 <param name="input_rod" type="data" format="vcf" label="Variant file (VCF format)" /> | |
| 95 </when> | |
| 96 <when value="custom"> | |
| 97 <param name="custom_rod_name" type="text" value="Unknown" label="Customer's variant file" /> | |
| 98 <param name="input_rod" type="data" format="vcf" label="Variant file (VCF format)" /> | |
| 99 </when> | |
| 100 </conditional> | |
| 101 </repeat> | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
102 |
|
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
103 <expand macro="allow_n_cigar_reads" /> |
| 0 | 104 <expand macro="gatk_param_type_conditional" /> |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
105 |
| 0 | 106 <expand macro="analysis_type_conditional"> |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
107 <param name="windowSize" type="integer" value="10" label="Window size for calculating entropy or SNP clusters (windowSize)" |
|
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
108 help="-window,--windowSize &lt;windowSize&gt;" /> |
|
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
109 <param name="mismatchFraction" type="float" value="0.15" label="Fraction of base qualities needing to mismatch for a position to have high entropy (mismatchFraction)" |
|
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
110 help="to disable set to <= 0 or > 1 (-mismatch,--mismatchFraction &lt;mismatchFraction&gt;)"/> |
|
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
111 <param name="minReadsAtLocus" type="integer" value="4" label="Minimum reads at a locus to enable using the entropy calculation (minReadsAtLocus)" |
|
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
112 help="-minReads,--minReadsAtLocus &lt;minReadsAtLocus&gt;" /> |
| 0 | 113 <param name="maxIntervalSize" type="integer" value="500" label="Maximum interval size" help="-maxInterval,--maxIntervalSize &lt;maxIntervalSize&gt;" /> |
| 114 </expand> | |
| 115 </inputs> | |
| 116 <outputs> | |
| 117 <data format="gatk_interval" name="output_interval" label="${tool.name} on ${on_string} (GATK intervals)" /> | |
| 118 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> | |
| 119 </outputs> | |
| 120 <tests> | |
| 121 <test> | |
| 122 <param name="reference_source_selector" value="history" /> | |
| 123 <param name="ref_file" value="phiX.fasta" ftype="fasta" /> | |
| 124 <param name="input_bam" value="gatk/fake_phiX_reads_1.bam" ftype="bam" /> | |
| 125 <param name="rod_bind_type_selector" value="dbsnp" /> | |
| 126 <param name="input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" /> | |
| 127 <param name="gatk_param_type_selector" value="basic" /> | |
| 128 <param name="analysis_param_type_selector" value="advanced" /> | |
| 129 <param name="windowSize" value="10" /> | |
| 130 <param name="mismatchFraction" value="0.15" /> | |
| 131 <param name="minReadsAtLocus" value="4" /> | |
| 132 <param name="maxIntervalSize" value="500" /> | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
133 <output name="output_interval" file="gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.gatk_interval" /> |
| 0 | 134 <output name="output_log" file="gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.log.contains" compare="contains"/> |
| 135 </test> | |
| 136 </tests> | |
| 137 <help> | |
| 138 **What it does** | |
| 139 | |
| 140 Emits intervals for the Local Indel Realigner to target for cleaning. Ignores 454 reads, MQ0 reads, and reads with consecutive indel operators in the CIGAR string. | |
| 141 | |
| 142 For more information on local realignment around indels using the GATK, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_indels_RealignerTargetCreator.html>`_. | |
| 143 | |
| 144 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_. | |
| 145 | |
| 146 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_. | |
| 147 | |
| 148 ------ | |
| 149 | |
| 150 **Inputs** | |
| 151 | |
| 152 GenomeAnalysisTK: RealignerTargetCreator accepts an aligned BAM input file. | |
| 153 | |
| 154 | |
| 155 **Outputs** | |
| 156 | |
| 157 The output is in GATK Interval format. | |
| 158 | |
| 159 | |
| 160 Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats. | |
| 161 | |
| 162 ------- | |
| 163 | |
| 164 **Settings**:: | |
| 165 | |
| 166 windowSize window size for calculating entropy or SNP clusters | |
| 167 mismatchFraction fraction of base qualities needing to mismatch for a position to have high entropy; to disable set to <= 0 or > 1 | |
| 168 minReadsAtLocus minimum reads at a locus to enable using the entropy calculation | |
| 169 maxIntervalSize maximum interval size | |
| 170 | |
| 171 @CITATION_SECTION@ | |
| 172 </help> | |
| 4 | 173 <expand macro="citations" /> |
| 0 | 174 </tool> |